Genomic engineering articles within Nature Communications

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  • Article
    | Open Access

    Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Here the authors present EspressionGAN, a generative adversarial network that uses genomic and transcriptomic data to generate regulatory sequences.

    • Jan Zrimec
    • , Xiaozhi Fu
    •  & Aleksej Zelezniak

  • Article
    | Open Access

    Thorough evaluation of CRISPR RNA-guided nucleases off-targets in cells is required for advancing gene therapies. Here the authors report SURRO-seq for the simultaneous investigation of thousands of off-target sites for therapeutic RNA-guided nucleases in cells.

    • Xiaoguang Pan
    • , Kunli Qu
    •  & Yonglun Luo

  • Article
    | Open Access

    The Sc2.0 consortia is reengineering the yeast genome. To expand the Sc2.0 genetic repertoire, the authors build a neo-chromosome comprising variable loci from diverse yeast isolates, providing phenotypic plasticity for use in synthetic backgrounds.

    • Dariusz R. Kutyna
    • , Cristobal A. Onetto
    •  & Anthony R. Borneman

  • Article
    | Open Access

    An efficient chassis for heterologous expression of biosynthetic gene clusters (BGCs) from Gram-negative bacteria is still unavailable. Here, the authors report rational construction of genome-reduced Burkholderials chassis to facilitate production of a class of new compounds by expressing BGC from Chitinimonas koreensis.

    • Jiaqi Liu
    • , Haibo Zhou
    •  & Xiaoying Bian

  • Article
    | Open Access

    Genome engineering will one day benefit from computational tools that can design genomes with desired functions. Here the authors develop computational design-simulate-test algorithms to design minimal genomes based on the whole-cell model of Mycoplasma genitalium.

    • Joshua Rees-Garbutt
    • , Oliver Chalkley
    •  & Claire Grierson

  • Perspective
    | Open Access

    Genome-scale engineering requires the integration of a wide range of in silico and in vivo technologies, as well data management procedures and legal infrastructure. Here the authors provide a list of recommendations to address these challenges.

    • Bryan A. Bartley
    • , Jacob Beal
    •  & Elizabeth A. Strychalski

  • Article
    | Open Access

    Construction of yeast libraries is time-consuming, costly and limited to the genetic background of the chosen strain. Here the authors present CASTLING which uses CRISPR-Cas12a and oligonucleotide pools to rapidly generate pooled libraries with large insertions such as fluorescent protein tags.

    • Benjamin C. Buchmuller
    • , Konrad Herbst
    •  & Michael Knop

  • Article
    | Open Access

    Genome structural variation can play an important functional role in phenotypic diversity. Here the authors use the SCRaMbLE system on a ring synthetic chromosome V to generate complex rearrangements distinct from a rearranged linear chromosome.

    • Juan Wang
    • , Ze-Xiong Xie
    •  & Ying-Jin Yuan

  • Article
    | Open Access

    The Sc2.0 project has built the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system into their synthetic chromosomes. Here the authors use SCRaMbLE to rapidly develop, diversify and screen strains for diverse production and growth characteristics.

    • B. A. Blount
    • , G-O. F. Gowers
    •  & T. Ellis

  • Article
    | Open Access

    SCRaMbLE has been used to rearrange synthetic chromosomes that have been introduced into host yeast. Here the authors produce semi-synthetic heterozygous diploid strains for rapid selection of phenotypes and map the rearrangements underlying selected phenotypes such as thermoresistance and caffeine resistance.

    • Michael J. Shen
    • , Yi Wu
    •  & Jef D. Boeke

  • Review Article
    | Open Access

    CRISPR has rapidly become an indispensable tool for biological research. Here Mazhar Adli reviews the current toolbox for editing and manipulating the genome and looks toward future developments in this fast moving field.

    • Mazhar Adli

  • Article
    | Open Access

    Genome-scale engineering is a powerful technique for understanding biology and designing microorganisms but has been limited to bacterial species. Here the authors present an automated platform for genome-scale engineering inSaccharomyces cerevisiaeusing CRISPR-Cas and RNAi.

    • Tong Si
    • , Ran Chao
    •  & Huimin Zhao

  • Article
    | Open Access

    The genome of some bacteria consists of two or more chromosomes or replicons. Here, diCenzo et al. integrate genome-scale metabolic modelling and growth data from a collection of mutants of the plant symbiont Sinorhizobium melilotito estimate the fitness contribution of each replicon in three environments.

    • George C. diCenzo
    • , Alice Checcucci
    •  & Marco Fondi

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